International Efforts in Nanoinformatics Research Applied to Nanomedicine

D. de la Iglesia; V. Maojo; S. Chiesa; F. Martin-Sanchez; J. Kern; G. Potamias; J. Crespo; M. Garcia-Remesal; S. Keuchkerian; C. Kulikowski; J. A. Mitchell

doi:10.3414/ME10-02-0012

Methods of Information in Medicine, Table of Contents

Methods Inf Med 2011; 50(01): 84-95
DOI: 10.3414/ME10-02-0012

Special Topic – Original Articles

Schattauer GmbH

International Efforts in Nanoinformatics Research Applied to Nanomedicine

D. de la Iglesia

¹Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Madrid, Spain

,

V. Maojo

¹Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Madrid, Spain

,

S. Chiesa

¹Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Madrid, Spain

,

F. Martin-Sanchez

²Department of Medical Bioinformatics. Institute of Health “Carlos III”, Madrid, Spain

,

J. Kern

³Department of Medical Statistics, Epidemiology and Medical Informatics, Andrija Stampar School of Public Health, Zagreb University Medical School, Zagreb, Croatia

,

G. Potamias

⁴Institute of Computer Science, FORTH, Heraklion, Crete, Greece

,

J. Crespo

¹Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Madrid, Spain

,

M. Garcia-Remesal

¹Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informatica, Universidad Politecnica de Madrid, Madrid, Spain

,

S. Keuchkerian

⁵HealthGrid Organization, Clermont-Ferrand, France

,

C. Kulikowski

⁶Department of Computer Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA

,

J. A. Mitchell

⁷Biomedical Informatics Department, University of Utah, Salt Lake City, UT, , USA

› Author Affiliations

Abstract

Summary

Background: Nanomedicine and nanoinformatics are novel disciplines facing substantial challenges. Since nanomedicine involves complex and massive data analysis and management, a new discipline named nanoinformatics is now emerging to provide the vision and the informatics methods and tools needed forsuch purposes. Methods from biomedical informatics may prove applicable with some adaptation despite nanomedicine involving different biophysical and biochemical characteristics of nanomaterials and corresponding differences in information complexity.

Objectives: We analyze recent initiatives and opportunities for research in nanomedicine and nanoinformatics as well as the previous experience of the authors, particularly in the context of a European project named ACTION-Grid. In this project the authors aimed to create a collaborative environment in biomedical and nanomedical research among countries in Europe, Western Balkans, Latin America, North Africa and the USA.

Methods: We review and analyze the rationale and scientific issues behind the new fields of nanomedicine and nanoinformatics. Such a review is linked to actual research projects and achievements of the authors within their groups.

Results: The work of the authors at the intersection between these two areas is presented. We also analyze several research initiatives that have recently emerged in the EU and USA context and highlight some ideas for future action at the international level.

Conclusions: Nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods in the nano-related areas. Opportunities for world-wide collaboration are already emerging and will be influential in advancing the field.

Keywords

Nanoinformatics - nanomedicine - nanoparticles - information management - text mining

Full Text

References

References
1 Jain KK. The Handbook of Nanomedicine. 1st ed. Totowa, New Jersey: Humana; 2008
2 Zerhouni E. Medicine: The NIH Roadmap. Science 2003; 302 5642 63-72. Available from: http://dx.doi.org/10.1126\%25252Fscience.1091867
3 National Institutes of Health, U. S.. Department of Health and Human Services. The NIH Roadmap: Accelerating Medical Discovery to Improve Health (homepage on the Internet). Maryland:: Division of Program Coordination, Planning, and Strategic Initiatives.; Updated February 2010; cited February 6, 2010. Available from: http://nihroadmap.nih.gov
4 Feynman R. There is plenty of room at the bottom. An Invitation to Enter a New Field of Physics. Engr & Sci 1960; 23: 22-36.
5 Buzea C, Pacheco II, Robbie K. Nanomaterials and nanoparticles: Sources and toxicity. Biointerphases 2008; 2 (04) MR17-MR71. Available from: http://dx.doi.org/10.1116/1.2815690
6 Weber DO. Nanomedicine. Health Forum J 1999; 42 (04) 32 36-37.
7 Douglas SJ, Davis SS, Illum L. Nanoparticles in drug delivery. Crit Rev Ther Drug Carrier Syst 1987; 3 (03) 233-261 (Review).
8 Kreuter J. Nanoparticles and nanocapsules – new dosage forms in the nanometer size range. Pharm Acta Helv 1978; 53 (02) 33-39.
9 Rogers JA. Recent developments in drug delivery. Can J Hosp Pharm 1982; 35 (06) 170-174 196.
10 El-Samaligy MS, Rohdewald P. Reconstituted collagen nanoparticles, a novel drug carrier delivery system. J Pharm Pharmacol 1983; 35 (08) 537-539.
11 Nilsson KG. Preparation of nanoparticles conjugated with enzyme and antibody and their use in heterogeneous enzyme immunoassays. J Immunol Methods 1989; 122 (02) 273-277.
12 Violante MR. Potential of microparticles for diagnostic tracer imaging. Acta Radiol Suppl 1990; 374: 153-156 (Review).
13 James ND, Coker RJ, Tomlinson D, Harris JR, Gompels M, Pinching AJ, Stewart JS. Liposomal doxorubicin (Doxil): an effective new treatment for Kaposi’s sarcoma in AIDS. Clin Oncol (R Coll Radiol) 1994; 6 (05) 294-296.
14 Truong-Le VL, August JT, Leong KW. Controlled gene delivery by DNA-gelatin nanospheres. Hum Gene Ther 1998; 9 (12) 1709-1717.
15 Freitas RA. Nanomedicine, Volume I: Basic Capabilities. Georgetown, Texas:: Landes Bioscience; 1999. Available from: http://www.nanomedicine.com/NMI.htm
16 Bogunia-Kubik K, Sugisaka M. From molecular biology to nanotechnology and nanomedicine. Bio-systems 2002; 65 2–3 123-138.
17 Roco MC. Nanotechnology: convergence with modern biology and medicine. Curr Op Biotechnol 2003; 14: 337-346.
18 Freitas RA. Nanomedicine, Volume IIA: Biocompatibility. Georgetown, Texas: Landes Bioscience; 2003. Available from: http://www.nanomedicine.com/NMIIA.htm
19 Allen TM, Cullis PR. Drug Delivery Systems: Entering the Mainstream. Science 2004; 303 5665 1818-1822. Available from: doi:10.1126/science. 1095833.
20 Jain KK, Jain V. Impact of nanotechnology on healthcare. Nanotechnol Law bus 2006; 3: 411-418.
21 Liu YY, Miyoshi H, Nakamura M. Nanomedicine for drug delivery and imaging: A promising avenue for cancer therapy and diagnosis using targeted functional nanoparticles. Int J of Cancer 2007; 120 (12) 2527-2537.
22 Gewin V. Big opportunities in a small world. Nature 2009; 460 7254 540-541.
23 Kulikowski CA. The micro-macro spectrum of medical informatics challenges: from molecular medicine to transforming health care in a globalizing society. Methods Inf Med 2002; 41 (01) 20-24.
24 Blobel B. Architectural approach to eHealth for enabling paradigm changes in health. Methods Inf Med 2010; 49 (02) 123-134.
25 Transinsight Gmb H. GoPubMed (homepage on the internet). Available from: http://www.gopubmed.org/ Last access: February 2010
26 Workshop on Nanoinformatics Strategies.. June 12-13, 2007. Westin Gateway Hotel, Arlington Virginia. Hosted by the National Nanomanufacturing Network. Available from: http://128.119.56.118/~nnn01/Workshop.html Last access: February 2010
27 Lopez-Alonso V, Hermosilla-Gimeno I, Lopez-Campos G, Maojo V, Martin-Sanchez FJ. Action GRID: assessing the impact of Nanotechnology on biomedical informatics. AMIA Annu Symp Proc 2008. p 1046
28 Thomas DG, Pappu RV, Baker NA. Ontologies for cancer nanotechnology research. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE, Sept. 3-4, 2009 pp 4158-4161.
29 caBIG Nanotechnology Working Group, National Cancer Institute.. Nanomedicine Ontology and Vocabulary (homepage on the internet). Available from: http://sites.google.com/site/cabignanowg/ontology-development-and-governance Last access: February 2010
30 FHDA and NASA.. Atlas of Nanotechnology (home-page on the internet). Available from: http://nanosense.org/documents/nanoed05/AtlasOf/Nanotechnology.pdf Last access: February 2010
31 Groen PJ, Wine M, Goldstein D. Implantable Medical Devices and EHR Systems. Virtual Medical records. 2007. Available from: http://www.hoise.com/vmw/07/articles/vmw/LV-VM-06-07-5.html
32 Network for Computational Nanotechnology, National Science Foundation.. NanoHub (home-page on the internet). Available from: http://nanohub.org Last access: February 2010
33 Towards Virtual Physiological Human: Multilevel modeling and simulation of the human anatomy and physiology.. White Paper edited by DG INFSO & DG JRC – November 2005. Available from: http://europa.eu.int/information_society/activities/health/docs/events/barcelona2005/ecvph-white-paper2005nov.pdf
34 Clapworthy G, Kohl P, Gregerson H, Thomas S, Viceconti M, Hose D. et al. Digital Human Modelling: A Global Vision and a European Perspective. In: Digital Human Modelling: A Global Vision and a European Perspective. Berlin: Springer; 2007. pp 549-558.
35 ACTION-Grid FP7 EC-funded Support Action.. ACTION-Grid (homepage on the internet). Available from: http://www.vph-action-grid.eu Last access: February 2010
36 Maojo V, Martin-Sanchez F, Kulikowski C, Rodriguez-Paton A, Fritts M. Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine. Pediatr Res 2010. (Epub ahead of print)
37 De la Iglesia D, Chiesa S, Kern J, Maojo V, Martin-Sanchez F, Potamias G, Moustakis V, Mitchell JA. Nanoinformatics: new challenges for biomedical informatics at the nano level. Stud Health Technol Inform 2009; 150: 987-991.
38 Chiesa S, De la Iglesia D, Crespo J, Martin-Sanchez F, Kern J, Potamias G, Maojo V. European efforts in nanoinformatics research applied to nanomedicine. Stud Health Technol Inform 2009; 150: 757-761.
39 De la Calle G, Garcia-Remesal M, Maojo V. A method for indexing biomedical resources over the internet. Stud Health Technol Inform 2008; 136: 163-168.
40 De la Calle G, Remesal MG, Chiesa S, de la Iglesia D, Maojo V. BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature. BMC Bioinformatics 2009; 10 (01) 320 +.
41 Chiesa S, García-Remesal M, de la Calle G, de la Iglesia D, Bankauskaite V, Maojo V. Building an Index of Nanomedical Resources: An Automatic Approach Based on Text Mining. Proc of the KES2008 (2). 2008 pp 50-57.
42 Rosamund D. et al. Insight: Lab on a chip. Nature 2006; 442 7101 367-418.
43 Yager P, Edwards T, Fu E, Helton K. et al. Micro-fluidic diagnostic technologies for global public health. Nature 2006; 442: 412-418.
44 Morris SK, Coombes KR, Koomen J. et al. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics 2005; 21: 1764-1775.
45 Yanagisawa K, Shyr Y, Xu BJ. et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003; 362: 433-439.
46 Gorelik E, Landsittel DP, Marrangoni AM, Modugno F, Velikokhatnaya L, Winans MT. et al. Multiplexed immunobead-based cytokine profiling for early detection of ovarian cancer. Cancer Epidemiol Biomarkers Prev 2005; 14: 981-987.
47 Mischak H, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JHH, Fliser D. et al. Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clinical Applications 2007; 1: 148-156.
48 LOCCANDIA FP6 EC-funded Project.. LOCCANDIA (homepage on the internet). Available from: http://www.loccandia.eu Last access: February 2010
49 Jordan B. et al. LOCCANDIA: Lab-on-Chip Based Protein Profiling for Cancer Diagnosis. In: Proc pHealth: International Workshop on Wearable Micro and Nanosystems for Personalised Health (full paper). Valencia, Spain; May 21-23, 2008
50 Kalaitzakis M, Kritsotakis V, Kondylakis H, Potamias G, Tsiknakis M, Kafetzopoulos D. An Integrated Clinico-Proteomics Information Management and Analysis Platform. In: Proc 21st IEEE International Symposium on Computer-Based Medical Systems (CBMS 2008), University of Jyväskylä, Finland,; pp 218-220. ISBN/ISSN: 1063-7125, 978-0-7695-3165-6.
51 Paulus C, Bonnet S, Gerfault L, Mery E, Strubel G, Ricoul F, Grangeat P. Chromatographic alignment combined with chemometrics profile reconstruction approaches applied to LC-MS data. In: Proc 29th Annual International Conference of the IEEE EMBS, (EMBC 2007), August 23-26, 2007, Lyon, France.: pp 5983-5986.
52 Pedrioliet PG. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004; 22 (11) 1459-1466.
53 Lin SM, Zhu L, Winter AO, Sasinowski M, Kibbe WA. What is mzXML good for?. Proteomics (Expert review) 2005; 2 (06) 839-845.
54 Lopez-Campos G, Coiras M, Sanchez-Merino JP, Lopez-Huertas MR, Spiteri I, Martin-Sanchez F, Perez-Brena P. Oligonucleotide microarray design for detection and serotyping of human respiratory adenoviruses by using a virtual amplicon retrieval software. J Virol Methods 2007; 145 (02) 127-136.
55 BussuB software, Institute of Health “Carlos III”.. Madrid (Spain) (homepage on the internet). Available from: http://ibsen.tic.udc.es/bussubWeb2 Last access: August 2010
56 Lopez-Campos GH, Garcia-Albert L, Martin-Sanchez F, Garcia-Saiz A. Analysis and management of HIV peptide microarray experiments. Methods Inf Med 2006; 45 (02) 158-162. Available from: http://www.schattauer.de/en/magazine/subject-areas/journals-a-z/methods/contents/archive/issue/677/manuscript/5942.html Last access: August 2010;
57 BRB-ArrayTools, Biometric Research Branch, National Cancer Institute (homepage on the internet). Available from: http://linus.nci.nih.gov/BRBArrayTools.html Last access: August 2010
58 Martín-Sanchez F, López-Alonso V, HermosillaGimeno I, Lopez-Campos G. A Primer in Knowledge Management for Nanoinformatics in Medicine. In: Proc KES 2008. Lecture Notes in Computer Science 2008; 5178: 50-57.
59 López-Alonso V, Moreno-López L, López-Campos G, Maojo V, Martin-Sanchez F. Description of an Ontology for supporting BIKMAS, a Biomedical Informatics Knowledge Management System. In: Proc KES 2002. IOS Press 2002. pp 955-959.
60 COMBIOMED Thematic Network.. Red COMBIOMED, (homepage on the internet). Available from: http://combiomed.isciii.es Last access: February 2010
61 European Commission.. Nanosciences, Nanotechnologies, Materials and new Production Technologies (homepage on the Internet). Available from: http://ec.europa.eu/research/fp7/index_en.cfm?pg=nano Last access: February 2010
62 European Technology Platform.. ETP Nanomedicine (homepage on the Internet). Available from: http://www.etp-nanomedicine.eu Last access: February 2010
63 Strategic Research Agenda for NanoMedicine.. European Technology Platform on NanoMedicine. November 2006. Available from: ftp://ftp.cordis.europa.eu/pub/nanotechnology/docs/nanomedicine_bat_en.pdf
64 SHARE FP6 EC-funded Project.. The SHARE Road-Map (homepage on the Internet). Available from: http://eu-share.org/roadmap/SHARE_roadmap_long.pdf Last access: February 2010
65 EGEE FP7 EC-funded Project.. EGEE Enabling Grids for E-SciencE (homepage on the Internet). Available from: http://www.eu-egee.org Last access: February 2010
66 DEISA FP7 e-INFRASTUCTURE EC-funded Project.. DEISA (Distributed European Infrastructure for Supercomputing Applications) (homepage on the Internet). Available from: http://www.deisa.eu Last access: February 2010
67 NorduGrid.. NorduGrid: Grid Solution for Wide Area Computing and Data Handling. (homepage on the Internet). Available from: http://www.nordugrid.org Last access: February 2010
68 National Science Foundation and the U. S.. Department of Energy’s Office of Science. OSG (Open Science Grid) (homepage on the Internet). Available from: http://www.opensciencegrid.org Last access: February 2010
69 National Cancer Institute, US National Institutes of Health.. caBIG: cancer Biomedical Informatics Grid (homepage on the Internet). Available from: https://cabig.nci.nih.gov Last access: February 2010
70 European Council.. ESFRI: European Strategy Forum on Research Infrastructures (homepage on the Internet). Available from: http://cordis.europa.eu/esfri/ Last access: February 2010
71 Saltz J, Oster S, Hastings S. et al. caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics 2006; 22 (15) 1910-1916.
72 Nanotechnology Characterization Laboratory, National Cancer Institute, US National Institutes of Health.. caNanoLab: cancer Nanotechnology Laboratory (homepage on the Internet). Available from: http://cananolab.abcc.ncifcrf.gov/caNanoLab/ Last access: February 2010
73 Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG. Nanotechnology Informatics White Paper. ca BIG, National Cancer Institute. February 2009 Non-peer Reviewed Manuscript
74 Alliance for NanoHealth (ANH).. Alliance for NanoHealth (homepage on the Internet). Available from: http://www.nanohealthalliance.org Last access: February 2010
75 National Institutes of Health.. The NIH Common Fund: National Network of Nanomedicine Development Centers (homepage on the Internet). Available from: http://nihroadmap.nih.gov/nanomedicine/fundedresearch.asp Last access: February 2010
76 Asia Pacific Nanotechnology Forum (homepage on the internet). Available from: http://www.apnf.org Last access: August 2010
77 Science and Technology Basic Plan, Japanese Council for Science and Technology Policy (homepage on the internet). Available from: http://www8.cao.go.jp/cstp/english/basic/ Last access: August 2010
78 Anon. 2007 Report on Mid- and Long-term Research and Development Strategy for Nanotechnology/Materials Science in Japan. Available at: http://www.nanonet.go.jp/english/info/report/rep20060628.html
79 Nanotechnology Researchers Network Center of Japan (homepage on the internet).. Available from: http://www.nanonet.go.jp/english Last access: August 2010
80 Center for Nano-Bio Integration at the University of Tokyo (homepage on the internet).. Available from: http://park.itc.u-tokyo.ac.jp/CNBI/e/index.html Last access: August 2010
81 Maojo V, Kulikowski C. Medical informatics and bioinformatics: integration or evolution through scientific crises?. Methods Inf Med 2006; 45 (05) 474-482.
82 Kuhn KA, Knoll A, Mewes HW, Schwaiger M. et al. Informatics and medicine – from molecules to populations. Methods Inf Med 2008; 47 (04) 283-295.
83 Altman RB, Balling R, Brinkley JF, Coiera E. et al. Commentaries on “Informatics and medicine: from molecules to populations”. Methods Inf Med 2008; 47 (04) 296-317.
84 Maojo V, Kulikowski CA. Reflections on biomedical informatics: from cybernetics to genomic medicine and nanomedicine. Stud Health Technol Inform 2006; 124: 19-24.
85 Mantas J, Ammenwerth E, Demiris G, Hasman A. et al. IMIA Recommendations on Education Task-Force.. Recommendations of the International Medical Informatics Association (IMIA) on Education in Biomedical and Health Informatics. First Revision. Methods Inf Med 2010; 49 (02) 105-120.
86 European Commission.. Nanosciences, Nanotechnologies, Materials and new Production Technologies Calls: FP7-NMP-2010-EU-USA (homepage on the Internet). Available from: http://cordis.europa.eu/fp7/dc/index.cfm?fuseaction=UserSite.CooperationDetailsCallPage&call_id=276 Last access: February 2010
87 U. S. Environmental Protection Agency.. Funding opportunities: Increasing Scientific Data on the Fate, Transport and Behavior of Engineered Nanomaterials in Selected Environmental and Biological Matrices – call EU-USA (homepage on the Internet). Available from: http://www.epa.gov/ncer/rfa/2010/2010_star_nano.html Last access: February 2010